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authorEfraim Flashner2022-01-27 17:09:42 +0200
committerEfraim Flashner2022-01-27 17:09:42 +0200
commit40dfce43b467e1ac99b85e003070d5107660dce4 (patch)
tree930dd26050232f9253ec31317692d00da8c5db6a /gn/packages/julia.scm
parentd1b682348601d968dd5ed3beb0049e7f51bb2c61 (diff)
downloadguix-bioinformatics-40dfce43b467e1ac99b85e003070d5107660dce4.tar.gz
gn: julia: Prepare packages for upstreaming
Diffstat (limited to 'gn/packages/julia.scm')
-rw-r--r--gn/packages/julia.scm200
1 files changed, 125 insertions, 75 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index ff1d7aa..f6856e0 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -1,5 +1,6 @@
(define-module (gn packages julia)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix download)
@@ -303,11 +304,10 @@ properties
(license license:expat)))
;; ready to upstream
-;; if the test suite passes
(define-public julia-optim
(package
(name "julia-optim")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method git-fetch)
@@ -316,24 +316,35 @@ properties
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0bv281n999kmjlp9p3vl4vv4phdl17z4gdpvkjzxsyk6dvcg2nrf"))))
+ (base32 "0nvl3xp9c6r80y9n7fic4zyq2443apfmbcpnx0wvgkv4vsy08x5j"))))
(build-system julia-build-system)
(arguments
- `(#:tests? #f ; TODO: Fix test
- ))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'adjust-tests
+ (lambda _
+ ;; TODO: Figure out why this test fails.
+ (substitute* "test/runtests.jl"
+ ((".*l_bfgs.*") "")))))))
(propagated-inputs
- `(("julia-compat" ,julia-compat)
- ("julia-fillarrays" ,julia-fillarrays)
- ("julia-linesearches" ,julia-linesearches)
- ("julia-nlsolversbase" ,julia-nlsolversbase)
- ("julia-nanmath" ,julia-nanmath)
- ("julia-parameters" ,julia-parameters)
- ("julia-positivefactorizations" ,julia-positivefactorizations)
- ("julia-statsbase" ,julia-statsbase)))
+ (list julia-compat
+ julia-fillarrays
+ julia-forwarddiff
+ julia-linesearches
+ julia-nanmath
+ julia-nlsolversbase
+ julia-parameters
+ julia-positivefactorizations
+ julia-statsbase))
(native-inputs
- `(("julia-measurements" ,julia-measurements)
- ("julia-optimtestproblems" ,julia-optimtestproblems)
- ("julia-recursivearraytools" ,julia-recursivearraytools)))
+ (list julia-linesearches
+ julia-measurements
+ julia-nlsolversbase
+ julia-optimtestproblems
+ julia-positivefactorizations
+ julia-recursivearraytools
+ julia-stablerngs))
(home-page "https://github.com/JuliaNLSolvers/Optim.jl")
(synopsis "Optimization functions for Julia")
(description "@code{Optim.jl} is a package for univariate and multivariate
@@ -655,12 +666,12 @@ R's d-p-q-r functions for probability distributions. It is a wrapper around
(("^ SKIPFILE.*") "")
(("^ #SKIPFILE") " SKIPFILE")))))))
(propagated-inputs
- `(("julia-nlsolversbase" ,julia-nlsolversbase)
- ("julia-nanmath" ,julia-nanmath)
- ("julia-parameters" ,julia-parameters)))
+ (list julia-nlsolversbase
+ julia-nanmath
+ julia-parameters))
(native-inputs
- `(("julia-doublefloats" ,julia-doublefloats)
- ("julia-optimtestproblems" ,julia-optimtestproblems)))
+ (list julia-doublefloats
+ julia-optimtestproblems))
(home-page "https://github.com/JuliaNLSolvers/LineSearches.jl")
(synopsis "Line search methods for optimization and root-finding")
(description "This package provides an interface to line search algorithms
@@ -671,7 +682,7 @@ implemented in Julia.")
(define-public julia-doublefloats
(package
(name "julia-doublefloats")
- (version "1.1.23")
+ (version "1.1.25")
(source
(origin
(method git-fetch)
@@ -680,18 +691,18 @@ implemented in Julia.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0qdkcmjknlan25dbgqw101zvgb5ly8v4pf1xikj6k2x96k8c6c8g"))))
+ (base32 "0cd3wxa2q77d9cxmi8gp5hpc95bfdf195mw03p6r1z543sfcfg0d"))))
(build-system julia-build-system)
(propagated-inputs
- `(("julia-genericlinearalgebra" ,julia-genericlinearalgebra)
- ("julia-polynomials" ,julia-polynomials)
- ("julia-quadmath" ,julia-quadmath)
- ("julia-requires" ,julia-requires)
- ("julia-specialfunctions" ,julia-specialfunctions)))
+ (list julia-genericlinearalgebra
+ julia-polynomials
+ julia-quadmath
+ julia-requires
+ julia-specialfunctions))
(native-inputs
- `(("julia-genericlinearalgebra" ,julia-genericlinearalgebra)
- ("julia-genericschur" ,julia-genericschur)
- ("julia-specialfunctions" ,julia-specialfunctions)))
+ (list julia-genericlinearalgebra
+ julia-genericschur
+ julia-specialfunctions))
(home-page "https://github.com/JuliaMath/DoubleFloats.jl")
(synopsis "Extended precision float and complex types")
(description "This package provides a math library with extended precision
@@ -702,7 +713,7 @@ floats and complex types.")
(define-public julia-polynomials
(package
(name "julia-polynomials")
- (version "2.0.14")
+ (version "2.0.24")
(source
(origin
(method git-fetch)
@@ -711,16 +722,17 @@ floats and complex types.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "07yb98fm9yhhan0n3iwmd9dz7zpj4kal99z5h1px1q5zpmjn68xa"))))
+ (base32 "1wpnk8m4l3ai7ggiim23xlvaxgbsjhprk614pva2pb4xi2jmclgq"))))
(build-system julia-build-system)
(propagated-inputs
- `(("julia-intervals" ,julia-intervals)
- ("julia-mutablearithmetics" ,julia-mutablearithmetics)
- ("julia-recipesbase" ,julia-recipesbase)))
+ (list julia-intervals
+ julia-mutablearithmetics
+ julia-recipesbase))
(native-inputs
- `(("julia-offsetarrays" ,julia-offsetarrays)
- ("julia-specialfunctions" ,julia-specialfunctions)
- ("julia-staticarrays" ,julia-staticarrays)))
+ (list julia-dualnumbers
+ julia-offsetarrays
+ julia-specialfunctions
+ julia-staticarrays))
(home-page "https://github.com/JuliaMath/Polynomials.jl")
(synopsis "Polynomial manipulations in Julia")
(description "This package provides basic arithmetic, integration,
@@ -768,7 +780,7 @@ polynomials.")
(define-public julia-timezones
(package
(name "julia-timezones")
- (version "1.5.5")
+ (version "1.7.1")
(source
(origin
(method git-fetch)
@@ -777,51 +789,89 @@ polynomials.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0f6rk1g4ffj4r6g8hfy0ygk4vyppibywkxgixhbgnc09w8y0009d"))))
+ (base32 "0sqckna9sivwxrhr7h7rmzmjxz3496q9yhd816y5z3b7vpv3gbqi"))))
(build-system julia-build-system)
(arguments
- `(#:tests? #f ; Tests attempt to download timezone information
- #:phases
- (modify-phases %standard-phases
- (add-after 'link-depot 'patch-tzdata
- (lambda* (#:key inputs #:allow-other-keys)
- ;(substitute* "src/tzdata/TZData.jl"
- ; (("(COMPILED_DIR = ).*" _ key)
- ; (string-append key "\"" (assoc-ref inputs "tzdata") "/share/zoneinfo\"")))
- (substitute* "test/runtests.jl"
- (("2016j") "2021a")
- ((".*download.jl.*") "")
- )
- (make-file-writable "Artifacts.toml")
- (with-output-to-file "Artifacts.toml"
- (lambda _
- (format #t "[tzdata2021a]~@
- git-tree-sha1 = \"6d94ada27957590cbd0d7678f5ae711232a4d714\"~@
- lazy = true~@
- ~@
- [[tzdata2021a.download]]~@
- sha256 = \"39e7d2ba08c68cbaefc8de3227aab0dec2521be8042cf56855f7dc3a9fb14e08\"~@
- url = \"file://~a\"~%"
- (assoc-ref inputs "tzdata-src"))))
- #t))
- )))
+ (list
+ #:tests? #f ; Tests attempt to download timezone information
+ ;#:phases
+ ;#~(modify-phases %standard-phases
+ ; (add-after 'link-depot 'patch-tzdata
+ ; (lambda* (#:key inputs #:allow-other-keys)
+ ; ;(substitute* "src/tzdata/TZData.jl"
+ ; ; (("(COMPILED_DIR = ).*" _ key)
+ ; ; (string-append key "\"" (assoc-ref inputs "tzdata") "/share/zoneinfo\"")))
+ ; (substitute* "test/runtests.jl"
+ ; (("2016j") "2021a")
+ ; ((".*download.jl.*") "")
+ ; )
+ ; (make-file-writable "Artifacts.toml")
+ ; (with-output-to-file "Artifacts.toml"
+ ; (lambda _
+ ; (format #t "[tzdata2021a]~@
+ ; git-tree-sha1 = \"6d94ada27957590cbd0d7678f5ae711232a4d714\"~@
+ ; lazy = true~@
+ ; ~@
+ ; [[tzdata2021a.download]]~@
+ ; sha256 = \"39e7d2ba08c68cbaefc8de3227aab0dec2521be8042cf56855f7dc3a9fb14e08\"~@
+ ; url = \"file://~a\"~%"
+ ; (assoc-ref inputs "tzdata-src"))))
+ ; #t))
+ ; )
+ ))
(propagated-inputs
- `(
- ("julia-lazyartifacts" ,julia-lazyartifacts)
- ("julia-mocking" ,julia-mocking)
- ("julia-recipesbase" ,julia-recipesbase)
- ))
+ (list
+ julia-inlinestrings
+ julia-mocking
+ julia-recipesbase))
(native-inputs
`(
;("julia-compat" ,julia-compat)
;("julia-timezones" ,julia-timezones)
;("curl" ,(@ (gnu packages curl) curl-minimal))
;("tzdata" ,(@ (gnu packages base) tzdata))
- ("tzdata-src" ,(package-source (@ (gnu packages base) tzdata)))
+ ;("tzdata-src" ,(package-source (@ (gnu packages base) tzdata)))
+ ))
+ (home-page "https://github.com/JuliaTime/TimeZones.jl")
+ (synopsis "IANA time zone database access for Julia")
+ (description "IANA time zone database access for the Julia programming
+language. @code{TimeZones.jl} extends the Date/DateTime support for Julia to
+include a new time zone aware @code{TimeType: ZonedDateTime}.")
+ (license license:expat)))
+
+(define-public julia-inlinestrings
+ (package
+ (name "julia-inlinestrings")
+ (version "1.1.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaStrings/InlineStrings.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0vr0hdig2vmgpnkxwhiw4wcl8pv69xyk0wpfig08sd6m8dg5wq4c"))))
+ (build-system julia-build-system)
+ (arguments
+ (list
+ #:tests? #f ; TODO: Fix skipping the test in question
+ ;#:phases
+ ;#~(modify-phases %standard-phases
+ ; (add-after 'unpack 'adjust-tests
+ ; (lambda _
+ ; (substitute* "test/runtests.jl"
+ ; ;; Need to skip lines 165, 166?
+ ; ((".*a,\".*") "") ; 165, 167
+ ; ((".*a__\".*") "") ; 166, 168
+ ; ))))
))
- (home-page "https://juliahub.com/docs/Infinity/")
- (synopsis "IANA time zone database access for the Julia programming language")
- (description "IANA time zone database access for the Julia programming language. TimeZones.jl extends the Date/DateTime support for Julia to include a new time zone aware TimeType: ZonedDateTime.")
+ (propagated-inputs
+ (list julia-parsers))
+ (home-page "https://github.com/JuliaStrings/InlineStrings.jl")
+ (synopsis "Fixed-width string types for Julia")
+ (description "This package provides fixed-width string types for
+facilitating certain string workflows in Julia.")
(license license:expat)))
;; ready to upstream, if we want